Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

2:37 PM Subject: Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4 Ni Hao, You don't give too much information here. What exactly are you doing? What are the commands? What's the difference between the first and the second pass of EM? One thing to c

Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

Ni Hao, You don't give too much information here. What exactly are you doing? What are the commands? What's the difference between the first and the second pass of EM? One thing to check is whether the output/input file has a correct box definition. Cheers, Tsjerk 2009/11/30 HAO JIANG : > Hi, >

[gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

Hi, I got a problem with the output structure files (gro/trr/xtc) generated by the energy minimization with GROMACS 4. That is, when I used the generated structure as the input for further minimizations or MD simulations, I got very large potential energy and forces at step 0, as if the structu